title: Insights from molecular modeling and dynamics simulation of pathogen resistance (R) protein from brinjal.
abstract: Resistance (R) protein recognizes molecular signature of pathogen infection and activates downstream hypersensitive response signalling in plants. R protein works as a molecular switch for pathogen defence signalling and represent one of the largest plant gene family. Hence, understanding molecular structure and function of R proteins has been of paramount importance for plant biologists. The present study is aimed at predicting structure of R proteins signalling domains (CC-NBS) by creating a homology model, refining and optimising the model by molecular dynamics simulation and comparing ADP and ATP binding. Based on sequence similarity with proteins of known structures, CC-NBS domains were initially modelled using CED- 4 (cell death abnormality protein) and APAF-1 (apoptotic protease activating factor) as multiple templates. The final CC-NBS structural model was built and optimized by molecular dynamic simulation for 5 nanoseconds (ns). Docking of ADP and ATP at active site shows that both ligand bind specifically with same residues and with minor difference (1 Kcal/mol) in binding energy. Sharing of binding site by ADP and ATP and low difference in their binding site makes CC-NBS suitable for working as molecular switch. Furthermore, structural superimposition elucidate that CC-NBS and CARD (caspase recruitment domains) domain of CED-4 have low RMSD value of 0.9 A° Availability of 3D structural model for both CC and NBS domains will . help in getting deeper insight in these pathogen defence genes.
authors.forename: Dipty
authors.initials: D
authors.lastname: Shrivastava
authors.forename: Vikrant
authors.initials: V
authors.lastname: Nain
authors.forename: Shakti
authors.initials: S
authors.lastname: Sahi
authors.forename: Anju
authors.initials: A
authors.lastname: Verma
authors.forename: Priyanka
authors.initials: P
authors.lastname: Sharma
authors.forename: Prakash Chand
authors.initials: PC
authors.lastname: Sharma
authors.forename: Polumetla Ananda
authors.initials: PA
authors.lastname: Kumar